Orlando Fraser QC, a former Conservative parliamentary candidate, emailed other board members and commission executives with his proposal when the media publicised the fact that the charity had in the past funded the controversial advocacy group Cage.

His email, part of a sequence disclosed in a recent court case, illustrates the active involvement of board members in an operational case, pushing for more robust regulation at a time when some charity leaders, lawyers and representative bodies are concerned about the commission’s growing focus on enforcement.

Other emails in the sequence say an inquiry was needed to send out "a strong message"; circulate critical articles about the JRCT in the Daily Mail, The Times and The Daily Telegraph; and make disparaging remarks about the charity’s commitment to non-violence. "How big of them," says one email by Fraser.

The sequence of emails began when Cage, which speaks up for what it calls victims of the war on terror, held a press conference at which it said it had in 2011 given advice to Mohammed Emwazi, also known as "Jihadi John", the British fighter for Islamic State who is believed to have beheaded several western hostages.

In an email sent on 27 February to Michelle Russell, director of investigations, monitoring and enforcement, and copied to Paula Sussex, the commission’s chief executive, Fraser called for an urgent statutory inquiry into whether any of JRCT’s funding of Cage had ended up supporting Jihadi John – and, if so, what the charity had known about it.

"If they fight it, so be it," he wrote. "It won’t be the worst thing to have to defend – and I suspect that they will in fact wish to be seen to cooperate. This is the form of robust regulation we have been talking about – legally (maybe) open to challenge, but fundamentally necessary, in the sector’s interests, heart in the right place, and would be 100 per cent supported and expected by the public.

"In these circumstances you would have this board member’s support (and the others)."

The same email to Russell and Sussex says: "I have understood and accepted your wish to follow the technical route until more turned up. However, the new information this week… requires a step change in approach to the robust (which the public will understand) and away from the technical (which they will not). It also shows that our original instincts were right, but that is easy with hindsight."

The email exchange included William Shawcross, chair of the commission, and three other board members: Peter Clarke, the former head of the anti-terrorist branch at the Metropolitan Police, the academic Gwythian Prins and the retired solicitor Tony Leifer.

Shawcross endorsed the course of action proposed by Fraser. "It is appalling, and Orlando is quite right," he wrote from Washington, where he said he was meeting senior US government counter-terrorism officials and analysts.

"One senior analyst also though it was astonishing that Cage was not long ago exposed for what it is – a jihadist front. We must be robust and, where possible, be seen to be robust, to protect the reputation of the sector as well as ourselves."

Cage denies that it supports terrorism.

In the event, the commission did not open a statutory inquiry, which gives it extensive powers over a charity and its assets. In 2013 it had already opened an operational compliance case, the result of which has not yet been published.

Instead, the commission successfully put pressure on the JRCT to make a commitment never to fund Cage again, which prompted Cage to seek a judicial review on the grounds that the commission had exceeded its powers. The commission has since contended that it had only offered advice and guidance to the JRCT.

The judicial review was withdrawn by Cage two weeks ago after a High Court hearing in front of the Lord Chief Justice, Lord Thomas, when the commission made a statement recognising that "it has no power to require trustees to fetter the future exercise of their fiduciary duties under its general power to give advice and guidance. In consequence, there is no obligation on the trustees of JRCT to fetter the proper and lawful exercise of their discretion in the future."

The internal emails by Fraser and others, disclosed as part of the proceedings, were mentioned in court by Helen Mountfield QC, representing the JRCT as an interested party, who called them "tendentious".

They were not read out or discussed in detail. A spokeswoman for the Charity Commission said: "We have not accepted – and nor has the court ruled – that they are relevant to the proceedings."

However, the Civil Procedure Rules say such documents lose confidentiality when they have been "read to or by the court, or referred to, at a hearing which has been held in public". The commission spokeswoman declined to comment on the content of the emails.

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